Problem: Resource buildings in a conquered town did not give me resources, then they fell within my sphere of influence but outside the city fence.
After taking over a town which had both a mine and a labor pit, I noticed that the town only produced 1 material. After 1 or 2 more turns I took over a nearby outpost just a few squares away. This resulted in the mine and a arcane tower being inside my sphere of influence but outside the city fence. Neither town/outpost got any materials or arcane research points for those two buildings. Neither could I destroy them or use them in any way, even though I they have been assimilated and operated with guys of my race...
Right now I have 3 saves which could illustrated the whole problem. One from just before I attacked the first town. One from when I have the town and the mine/tower but without getting the benefits of them. And one from when they are outside the city fence...
First save (Before attacking the city) http://filebin.ca/pfvqh/Goingtowar.EleSav
Second save (After taking city, here you can see that the mine does not give me mats...) http://filebin.ca/dwhfuv/PreviousAutoSave.EleSav
Third save (Now the mine and arcane tower are inside influence sphere but outside the city fence) http://filebin.ca/bueqwr/temp.EleSav
Game/Computer info: I have no mods and the game fully updated, I use the latest drives for a HD5800 card with win7 64bit.